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paleoanthropology, genetics and evolution

Egypt

  • Mummy trouble redux

    Thu, 2011-04-28 22:56 -- John Hawks

    Speaking of Jo Marchant, she has a long article in the current Nature about the mummy DNA controversy ("Ancient DNA: Curse of the Pharoah's DNA").

    I wrote about the problem earlier this year: "Mummy troubles". My opinion is that this work has been relentlessly hyped and hasn't presented adequate information to assess whether the results are genuine:

    Can we accurately type STR alleles from mummies? I wouldn't rule it out given the quantity of tissue available, but there should be many more controls for a high-profile study like this one. The work took place over several years, so it's a bit unrealistic to expect the latest sequencing methods. But JAMA and the Discovery Channel presented the results as important science. They should have ensured that solid answers for the obvious questions were at hand.

    Marchant digs up some quotes from the authors:

    The researchers deny that the television involvement put them under excessive pressure to produce dramatic results. But working for the cameras did make a challenging project even tougher, says Pusch. "Each time they came in to film, we had to close the lab for a week to clean." Eventually the TV crew was banished and the lab scenes reconstructed.

    The article gives an interesting sociology of the competing groups of ancient DNA researchers. I dispute that the field is evenly divided, however. There are a very long list of laboratories doing ancient DNA work according to standardized protocols on skeletal remains from the past several thousand years. Only a few groups claim to be working with nuclear DNA or microbial DNA, the areas of contention in the mummies. Among that small set of labs, most follow similar, conservative techniques.

    Then there are the handful that come up with "surprising" results time and again. If the surprising results are accompanied by substantial evidence, I have no problem. But when a paper has no clear explanation why it arrives at results that others think impossible, that raises my skepticism.

    Tags: 
    ancient DNA
    history
    Egypt

  • Mummy troubles

    Sun, 2011-01-23 01:32 -- John Hawks

    Mummies are always trouble. I hate to say it. You see, in my line of work we can do an awful lot with a skeleton. We're usually down to a few pieces of bone, so that a skeleton is an unimaginable luxury.

    The typical mummified body carries so much more information than a skeleton. I mean, you've got soft tissue there, whole organs. Food left in the mummy's tummy. With Egyptian mummies, you had a whole crew of embalmers using special techniques to preserve the body. They could not possibly have done more to give us time capsules of human biology from the dawn of history.

    So why does it seem like every study of a mummy ends up in a fight?

    I think that mummies give too much to chew on. With a bone, it's sort of likely that you only have one indicator of pathology. One symptom makes for a pretty simple diagnostic problem. Sure, you're likely to be wrong, but with one symptom where's the argument?

    Now, a whole body -- well, there you'll probably have several symptoms. Or you'll have things you would expect to see with a pathology, but they're just not there. So every armchair paleopathologist ends up with his own theory about what the mummy's got.

    The mummies in the news this week are thought to be Akhenaten, Tutankhamen, and their relatives. Last year, Zahi Hawass and colleagues [1] published a paper in the Journal of the American Medical Association, reporting on their Discovery Channel-funded research on these mummies. They ran a series of tests to assess the paleopathology of these mummies, including some work demonstrating the presence of falciparum malaria. They also extracted DNA from the mummies and constructed a pedigree connecting them based on shared microsatellite alleles.

    I wouldn't ordinarily write about mummies. They're really not my thing. If there were a Neandertal mummy, well, I'd be all over that. Ain't gonna happen.

    But if you follow ancient DNA, that last detail probably gave you a bit of a hiccup. Can we really amplify STR alleles from mummies with any accuracy?

    Well, that's why the story is in the news this week. For example, Jo Marchant in New Scientist writes "Royal rumpus over King Tutankhamun's ancestry", quoting geneticists who question the results. Eline Lorenzen and Eske Willerslev wrote a letter to JAMA pointing out the literature on the topic [2]. There are just so many problems with contamination and DNA degradation, even if you have a large tissue sample to work with. The idea that you could extract DNA and do straight-up PCR amplification to identify microsatellite alleles seems, well, optimistic.

    The geneticists involved in the study, Albert Zink and Carsten Pusch, defend their approach in a published reply, as well as in the New Scientist piece.

    I'm skeptical. In 2000, Pusch was involved in a study that claimed to extract DNA from Neandertal and early modern human remains, testing their similarity by means of Southern hybridization [3]. That's an even simpler technique, and the published result surprised a lot of people. Cooper and Poinar [4] immediately criticized the study for lacking the proper controls. Shortly afterward, Geigl [5] challenged the result by demonstrating the strength of results could not have emerged among closely-related primate species and likely reflected the presence of soil microorganisms. Considering what we now know about the low endogenous DNA content of ancient skeletal remains, DNA-DNA hybridization just couldn't possibly have gotten any result that wasn't noise.

    That's the kind of problem that emerges regularly with ancient DNA studies. When someone is taking an approach outside of the ordinary, they'd better document extremely well their attempts to quantify contamination and present many different approaches to validate their results. At a minimum it is very surprising that mtDNA sequence data were not available with the initial results. The lack of adequate documentation in the Hawass study is why a controversy is arising now.

    Can we accurately type STR alleles from mummies? I wouldn't rule it out given the quantity of tissue available, but there should be many more controls for a high-profile study like this one. The work took place over several years, so it's a bit unrealistic to expect the latest sequencing methods. But JAMA and the Discovery Channel presented the results as important science. They should have ensured that solid answers for the obvious questions were at hand.

    References

    1. Hawass Z, Gad YZ, Ismail S, Khairat R, Fathalla D, Hasan N, Ahmed A, Elleithy H, Ball M, Gaballah F, et al. Ancestry and Pathology in King Tutankhamun's Family. JAMA: The Journal of the American Medical Association [Internet]. 2010;303:638–647. Available from: http://dx.doi.org/10.1001/jama.2010.121
    2. Lorenzen ED, Willerslev E. King Tutankhamun's Family and Demise. JAMA: The Journal of the American Medical Association [Internet]. 2010;303:2471. Available from: http://dx.doi.org/10.1001/jama.2010.818
    3. Scholz M, Bachmann L, Nicholson G, Bachmann J, Giddings I, Ruschoffthale B, Czarnetzki A, Pusch C. Genomic Differentiation of Neanderthals and Anatomically Modern Man Allows a Fossil–DNA-Based Classification of Morphologically Indistinguishable Hominid Bones. The American Journal of Human Genetics [Internet]. 2000;66:1927–1932. Available from: http://dx.doi.org/10.1086/302949
    4. Cooper A, Poinar HN. Ancient DNA: do it right or not at all. Science (New York, N.Y.) [Internet]. 2000;289. Available from: http://view.ncbi.nlm.nih.gov/pubmed/10970224
    5. Geigl EM. Inadequate use of molecular hybridization to analyze DNA in Neanderthal fossils. American journal of human genetics [Internet]. 2001;68:287–291. Available from: http://dx.doi.org/10.1086/316948
    Tags: 
    ancient DNA
    history
    Egypt

  • The paleolakes of Egypt

    Fri, 2010-12-03 13:08 -- John Hawks

    A paper in the December issue of Geology, by Ted Maxwell and colleagues [1], describes evidence for a "Lake Erie-sized" paleolake in southwestern Egypt. The existence of a large ancient lake has been suspected for many years based on the presence of fish fossils in Middle Pleistocene contexts far from any current body of water. The new paper uses range-sensing imagery to assess the likely extent of the paleolake from elevation data, one known occurrence of fish fossils, and landscape features that appear to substantiate an ancient lake terrace:

    We believe that the middle and late Pleistocene drainage was influenced by repeated Nile flooding, following on the working hypothesis of Haynes (1985), who suggested a large Pleistocene lake that drained into the Nile from what he termed the Kiseiba-Dungul depression. Using the elevation of the fossil (Middle Paleolithic) Nilotic fish found at Bir Tarfawi (Van Neer, 1993) as a base level, the SRTM data indicate that a paleolake at that level (247 m) would have flooded the entire Kiseiba-Tushka depression (Fig. 3), and is the same elevation at which the Selima paleochannels and other channel remnants to the west blend into the terrain (Fig. 2). We interpret the combination of topographic coincidence and ages of Middle Paleolithic occupations at Selima and Tarfawi as evidence of at least one lake level at that elevation, forming a local base level, reducing the competence of inflowing streams, and inhibiting channel incision below ∼247 m. Such a lake would have covered an area of 68,200 km2, and would have extended from the Sudan border (22°N) north to the Kharga and Dakhla Oases, until dammed by the limestone plateau at 26°N.

    They believe that the lake would have been filled by Nile outflow. The paper does not commit to any chronology, except to point out that a few late Acheulean sites are present in the basin near a presumed lower lake level of 190 m, which may represent a relatively stable size, flooded once or multiple times to the higher level of 247 m. Wired has a nice short description of the paper, which includes some dates that are not actually discussed in the paper.

    A better understanding of the Nile corridor is of course very important to the issue of human movement into and out of Africa during the Late Pleistocene. More recent Late Pleistocene and Holocene paleolakes are known up and down the Nile valley, from the Fayum to Darfur.

    I wonder if a Nile corridor that was ostensibly more habitable may have actually excluded gene flow back into Africa. A denser and more stable human population in this area would have been a relative population source much of the time, sending migrants out into adjacent regions. These regions would have been much less habitable at some times, but displacement of the large Nile valley population may have been impossible. Furthermore, a larger Nile corridor population would have been a reservoir for endemic parasites and diseases that would have posed challenges for migrants into the region.

    The problem on an evolutionary timescale is not getting people out of Africa, but explaining the level of population structure between regions that constantly shared an overland and shoreline connection.

    References

    1. Maxwell TA, Issawi B, Haynes VC. Evidence for Pleistocene lakes in the Tushka region, south Egypt. Geology [Internet]. 2010;38:1135–1138. Available from: http://dx.doi.org/10.1130/G31320.1
    Tags: 
    Africa
    Middle Pleistocene
    paleoclimate
    Egypt
    geology
    Synopsis: 
    Acheulean-era people may have lived along an Erie-sized lake in the Nile corridor.

  • Quote: Osborn on the Fayum beds

    Tue, 2009-08-25 08:30 -- John Hawks

    Another passage from Henry Fairfield Osborn, "Hunting the ancestral elephant in the Fayûm desert":

    As we ascended, we noted suddenly the entire disappearance of the sea-shells, adn entered purely freshwater desposits, where the land-filling process gained supremacy. We climbed tier above tier, and finally reached the great, partly level, partly rolling, platform stretching off in each direction as far as the eye could reach. Here we saw the sandy delta deposits of a river system which was much older than the Nile.

    This was our destination.

    We slowly recognized this as the level on which all our explorations were to be made. The giant trunks of fossilized trees began to appear -- trees that were borne down the rivers from the great forests of the south, their petrified trunks, from thirty to seventy feet in length, protruding from the sand, which was an auspicious sign of the proximity of the remains of quadrupeds, for both were washed down together. Remains of crocodiles, also, and of great turtles, began to be seen, and we were convinced that we were in the very fossil-bearing tier itself.

    I will note an impression I had while reading the article, that it's very interesting to see how paleontologists dealt with certain issues in the time before acceptance of continental drift. The passage immediately before the one quoted here dealt with the "northward growth" of Africa into the Mediterranean, from the Fayum to the present coast, entirely as a process of river discharge.

    References:

    Osborn HF. 1907. Hunting the ancestral elephant in the Fayûm desert: Discoveries of the recent African expedition of the American Museum of Natural History. The Century Magazine 74(6):815-835.

    Tags: 
    Henry Fairfield Osborn
    quotes
    Africa
    Fayum
    history of paleontology
    Egypt

  • Quote: Osborn on the reception of bug-hunters

    Mon, 2009-08-24 08:30 -- John Hawks

    More from Henry Fairfield Osborn, "Hunting the ancestral elephant in the Fayûm desert":

    News of the approach of an important caravan under government patronage had preceded us, and in the village of Tamia, on the Sunday evening of our arrival, began a display of Oriental hospitality, with formal visits of respect, and presentation of gifts, which continued throughout our whole stay in the desert to the north. An elderly sheikh, Harun Talasun, called in the evening with ten attendants, and in the morning returned with a donkey, led by a slave and bearing a fine sheep. The corpulent Mamour of the district at frequent intervals sent mounted men to inquire after our comfort, and invited us to a feast. An Arab, Mahmud Abd-el-Baqui, visited us in the desert, accompanied by two brothers and an armed escort, bringing us a sheep and turkeys, and on the casual expression of a desire, returned to camp with five spirited and perfectly trained horses, each with its attendant. These hospitable places of fossil-hunting in the Libyan desert were in delightful contrast to former experiences in America. Imagine the mayor, or the sheriff, or the aldermen of a Western town showing such solicitude for a party of "Eastern bug-hunters" or "bone-diggers!" One must find coal, or oil, or gold, to command the admiration of our good-hearted, but too practical-minded countrymen. Throughout our prolonged stay in Egypt we learned to love and admire these simple people. They are ignorant and somewhat crafty, through ages of misrule, but perhaps we have more to learn from them than they from us. As I told Lord Cramer on my return, the kindly attitude toward us always exhibited by the common people was to my mind the strongest proof of the popularity of English rule among the masses of the people of Egypt.

    Uh...OK, then.

    I highlighted the part above because it is such a great line -- but also to note that Tocqueville read the matter more accurately than Osborn. I think I like the idea of Americans unimpressed with "an important caravan under government patronage."

    Although in reality a crew of fifty men led by Henry Fairfield Osborn going through my Western hometown would have brought more excitement than anything short of the Ringling Brothers.

    References:

    Osborn HF. 1907. Hunting the ancestral elephant in the Fayûm desert: Discoveries of the recent African expedition of the American Museum of Natural History. The Century Magazine 74(6):815-835.

    Tags: 
    quotes
    Africa
    Fayum
    history of paleontology
    Egypt
    Henry Fairfield Osborn

  • Quote: Osborn on biogeography

    Thu, 2009-08-06 20:01 -- John Hawks

    Henry Fairfield Osborn, "Hunting the ancestral elephant in the Fayûm desert":

    One of the most fascinating problems of paleontology, therefore, is to ascertain the birthplace of each of the great animal groups -- the fertile or arid nursery wherein they first took on their peculiar and characteristic form, and, like the races of man, felt the power and strength to go forth and invade the lands of other races.

    References:

    Osborn HF. 1907. Hunting the ancestral elephant in the Fayûm desert: Discoveries of the recent African expedition of the American Museum of Natural History. The Century Magazine 74(6):815-835.

    Tags: 
    biogeography
    Fayum
    quotes
    Africa
    history of paleontology
    Egypt
    Oligocene

  • Shamone

    Thu, 2009-08-06 19:04 -- John Hawks

    Funny, this didn't stand out to me at the Field when we were there last...

    It's eerie, and it's creepy: An ancient limestone Egyptian bust in the Field Museum is a dead bang look-a-like of singer Michael Jackson.

    Uh...wait for it...

    The curiosity: The nose of the ancient Egyptian statue, which has been in the museum's private collection since 1899, is disintegrating. At the end of his life, Jackson's nose appeared to be disintegrating.

    It does look weirdly like Michael Jackson. (A larger picture from NPR)

    Tags: 
    Egypt
    humor
    celebrities
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